Biology Stage 2 - DNA and Proteins

What is the function of DNA?

To store and transmit genetic information

What is the structure of DNA?

Double helix

What are nucleotides made of?

Phosphate, sugar, nitrogen base (A,T,C,G)

What are base pairing rules?

A-T and C-G

What bonds hold DNA strands together?

Weak hydrogen bonds

Why are weak bonds important?

Allow DNA to unzip for replication

What is semi-conservative replication?

One original strand and one newly synthesised strand

What direction is DNA read?

5' to 3' direction

Describe eukaryotic DNA

Linear, bound to histones, forming chromosomes. In nucleus.

Describe prokaryotic DNA

Unbound and circular, in cytosol

What is a gene?

Sequence of DNA coding for protein or RNA

What are the stages of protein synthesis?

Transcription and translation

Where does transcription occur?

Nucleus

What is produced in transcription?

mRNA molecule.

Where does translation occur?

Ribosome - outside of nucleus

Role of mRNA

Carries genetic code

Role of tRNA

Brings amino acids

Role of rRNA

Forms ribosome

What are exons?

Coding regions

What are introns?

Non-coding regions removed

What is a codon?

3-base sequence for amino acid

What is an anticodon?

Complementary tRNA sequence

What determines protein shape?

Amino acid sequence

Why is protein shape important?

Determines function

4 levels of protein structure

Primary, secondary, tertiary, quaternary

What is an enzyme?

Biological catalyst - speeds up reactions.

How do enzymes work?

Lower activation energy

What is enzyme specificity?

Only binds specific substrate

What is the induced fit model?

Enzyme changes shape to fit substrate

Factors affecting enzymes

Temperature, pH, inhibitors

What happens at high temperature?

Denaturation

The rate of an enzyme controlled reaction is affected by?

Concentration of reactants and concentration of the enzyme.

What is gene expression?

Production of proteins from genes

What affects gene expression?

Environment and transcription factors

What is cell differentiation?

Cells become specialised

What is epigenetics?

Gene expression changes without DNA change

Epigenetic examples

DNA methylation, histone modification

What is a mutation?

Change in DNA sequence

Causes of mutation

Errors, radiation, chemicals, viruses

What are germ mutations?

Inherited

What are somatic mutations?

Not inherited

What is PCR?

DNA amplification

Steps of PCR

1. Denaturing - Heat DNA to 95oC, breaking weak hydrogen bonds and exposing bases.

2. Annealing - Cool to 60oC, this allows primers to attach to bases.

3. Extension - Heat to 72oC, Add free nucleotides and Taq DNA Polymerase which joins the free nucleotides with the original strands.

What is Taq DNA Polymerase?

A heat stable DNA Polymerase

What is electrophoresis?

A technique used to separate DNA fragments based on size and charge to leave a unique pattern

What happens to smaller fragments?

Move further

What is DNA profiling?

Identifying individuals without mapping the entire genome

What are restriction enzymes?

Enzymes that recognise and cut at particular base sequences.

What are vectors?

Carry genes (plasmids/viruses)

Steps of DNA Replication

1. An enzyme called helicase unzips the DNA

2. An enzyme called DNA polymerase builds the new strand in a 5’ to 3’ direction.

3. 2 new identical strands of DNA are formed.

Exons and introns

Both are transcribed, but introns are spliced out and only exons are translated.

Transcription

1. RNA Polymerase unzips the DNA, breaking weak hydrogen bonds and exposing bases.

2. Free RNA nucleotides (A,U,G,C) join the genes bases on the strand, forming a mRNA molecule.

3. The mRNA molecule leaves the nucleus via a nuclear pore.

4. The DNA zips back up, unaltered.

Translation

1. mRNA binds to a ribosome

2. tRNA molecules contain an anti codon, which corresponds to a specific amino acid which is brought to the mRNA strand.

3. The tRNA anti codon binds to its complementary base pairing with the mRNA codon.

4. Ribosome joins the amino acid together with peptide bonds to form a polypeptide chain.

5. The polypeptide chain moves away from the ribosome into the rough endoplasmic reticulum and folds into its final protein shape.

Primary Structure

The unique sequence of amino acids in the polypeptide chain joined with peptide bonds.

Secondary Structure

The coiling or folding of localised sections of the polypeptide chain. Helix or pleated sheet.

Tertiary Structure

A 3D shape of the polypeptide chain.

Quaternary Structure

2 or more polypeptide chains bonded together.

Competitive inhibitor

Inhibitor that binds to the active site

Non-competitive inhibitor

Attatches to the enzyme in areas other than the active site

What is an inhibitor?

Chemicals which inhibit the enzyme from producing its final product.

Proteins with specific shapes

Enzymes, some hormones, receptor proteins, antibodies.

How is the folding of a polypeptide into a protein determined?

By its sequence of amino acids

What determines phenotypic expression of genes?

Phenotypic expression depends on regulation of transcription and translation, influenced by transcription factors, other gene products, and environmental factors

What are transcription factors?

Proteins that bind to DNA and regulate the rate of transcription of specific genes

How does the environment influence gene expression?

Environmental factors such as temperature, nutrients, or chemicals can activate or suppress gene expression

What controls cellular differentiation?

Differential gene expression, where certain genes are turned on or off in specific cells

What is cellular differentiation?

The process by which cells become specialised in structure and function

How is tissue growth and development controlled?

By selective expression of genes that determine cell structure and function during development

What are epigenetic changes?

Heritable changes in gene expression that do not involve changes to the DNA sequence

How can epigenetics cause differences in identical siblings?

Differences in DNA methylation and histone modification can alter gene expression despite identical DNA

How can epigenetics differ between clones?

Environmental influences can lead to different epigenetic modifications, resulting in different phenotypes

How can epigenetics contribute to disease?

Abnormal gene expression caused by epigenetic changes can disrupt normal cellular function and lead to disease

What is DNA methylation?

The addition of methyl groups to DNA, usually reducing gene expression by preventing transcription

What is histone modification?

Chemical changes to histone proteins that affect how tightly DNA is wound and its accessibility for transcription

How do epigenetic changes affect gene expression?

They alter how accessible DNA is to transcription machinery, turning genes on or off without changing sequence

How can DNA methylation lead to cancer?

Hyper-methylation may silence tumour suppressor genes, while hypo-methylation may activate oncogenes, disrupting cell cycle control

What are tumour suppressor genes?

Genes that normally regulate and prevent uncontrolled cell division

What are oncogenes?

Mutated genes that promote excessive cell division and can contribute to cancer

What is the difference between germ cell mutations and somatic cell mutations?

Germ cell mutations are inheritable and passed to offspring, while somatic mutations affect only the individual and are not inherited

What are the consequences of germ cell mutations?

They can be passed on to descendants and affect future generations

What are the consequences of somatic cell mutations?

They may affect the individual (e.g. cancer) but are not inherited

What is DNA extraction?

The process of isolating DNA from cells using chemical and mechanical methods

How is DNA extracted from cells?

Cells are lysed to release DNA, proteins are removed, and DNA is purified using alcohol precipitation

What is gel electrophoresis?

A technique used to separate DNA fragments based on size using an electric current

How does gel electrophoresis work?

DNA fragments are placed in a gel, an electric current is applied, and fragments move toward the positive electrode, with smaller fragments moving further

What is an electropherogram?

A graphical representation of DNA fragments produced by electrophoresis or sequencing, showing peaks corresponding to fragment sizes or bases

How is DNA sequencing used?

It determines the exact order of nucleotides in a DNA molecule

What is genome mapping?

The process of determining the complete DNA sequence of an organism’s genome

How are electrophoresis results used in DNA profiling?

They produce banding patterns or electropherograms that represent an individual’s unique DNA profile

What is DNA profiling?

A technique used to identify individuals based on unique patterns in their DNA

Why is DNA profiling unique?

Because individuals have unique combinations of STRs (short tandem repeats)

What are STRs?

Short tandem repeats are repeating sequences of DNA that vary in number between individuals

How is DNA profiling used in forensic science?

It compares DNA samples from crime scenes with suspects to identify matches

What are vectors in biotechnology?

Tools such as plasmids or viruses used to transfer genetic material into cells

What is a plasmid?

A small circular DNA molecule in bacteria used as a vector in genetic engineering

What are viruses used for in biotechnology?

They can act as vectors to deliver genetic material into host cells

What are bacterial transformation techniques?

Methods used to introduce foreign DNA into bacteria

What is electroporation?

A technique that uses an electric pulse to create temporary pores in cell membranes to allow DNA entry

What is microinjection?

The direct injection of DNA into a cell using a fine needle

How are restriction enzymes used in gene selection?

They cut DNA at specific sequences to isolate desired genes